plotByGroup: Visualize one categorical column and one numeric column

In RIVM-IIV-Microbiome/biomeViz: Data visualization for microbiome analytics

Visualize one categorical column and one numeric column

Description

Visualize one categorical column and one numeric column

Usage

plotByGroup(x, x.factor = NULL, y.numeric = NULL)

Arguments

x	phyloseq-class object.
x.factor	A column in sample_data to compare that is a factor
y.numeric	A column in sample_data to compare that is a numeric

Details

A simple plotting utility for visualization of one categorical and numerical variable. Provided a categorical variable and numerical variable present in sample_data of a phyloseq-class object, a comparative visualization can be done.

Value

a ggplot object.

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeViz

Examples

library(biomeUtils)
library(biomeViz)
library(dplyr)
library(microbiome)
library(ggplot2)
ps <- FuentesIliGutData
# calculate Shannon diversity using microbiome::diversity and add it to
# the sample_data in phyloseq using biomeUtils::mutateSampleData()
ps <- mutateSampleData(ps,
                       Shannon = microbiome::diversity(ps, "shannon")[,1])
plotByGroup(ps,
            x.factor="ILI",
            y.numeric = "Shannon") +
         geom_point(aes(color=ILI),
                    position = position_jitter(width = 0.1)) +
         scale_color_manual(values=c("steelblue", "brown3", "grey70"))

RIVM-IIV-Microbiome/biomeViz documentation built on July 20, 2022, 3:52 a.m.